I have noticed one change with the Black Box edition: 2 order cards of the same color can be played as a Jack as opposed to the older rules which required 3 order cards.

Well there are two sets of rules. The original game (Imperium rules in BB) were very cut-throat and difficult for new players. Then there was an unofficial-offical, variant (Republica rules in BB) that was then used by a lot of people that was originally developed by people playing MIT I believe (see TOP SECRET – Do Not Read). It changed a couple of cards and used the 2 order card rule, making things a little easier on players. The Black Box comes with rules and cards for both rules, and the differences are shown here: